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Sachini Weerasekara
weerasekara.s [AT] northeastern [DOT] edu
I am a PhD student in machine learning at Northeastern University, Boston, MA, where I am fortunate to be advised by Prof. Jacqueline Isaacs
and Prof. Sagar Kamarthi.
I previously earned my master’s degree at Northeastern University, Boston, MA and my bachelor’s degree from the University of Moratuwa, Sri Lanka.
I have also spent time doing machine learning research, applied AI, and building data pipelines at Takeda Pharmaceuticals, Dell Technologies, Aikium Inc , and EFL Global.
My research is focused on developing machine learning methods for scientific discovery, with applications spanning human biology, biological design, and autonomous systems.
To this end, I develop methods that carry even small amounts of high-value signals much further in learning systems to generalize more effectively even with limited data.
Across these problems, I am interested in the full machine learning lifecycle from building data and experimentation pipelines and analyzing large-scale datasets to developing, evaluating, and deploying models.
Ultimately, my goal is to develop machine learning methods that enable models to learn robust representations, generalize beyond their training distributions, and remain reliable in real-world deployment.
LinkedIn  | 
Github  | 
Google Scholar  | 
CV
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| Sep |
2026 |
Our work on post-pretraining for alignment in single cell foundation models is out! Check it out here! |
| Sep |
2026 |
Our work on iterative action refinement for continuous control policies is out! Check it out here! |
| Dec |
2025 |
I will be at NeurIPS 2025! |
| July |
2025 |
I am joining Aikium Inc as a machine learning scientist intern to work on generative model fine-tuning for drug discovery. |
| Apr |
2025 |
Our work on policy learning for optimizing robotic disassembly lot sizing with reinforcement learning was accepted at Journal of Advanced Manufacturing and Processing. |
| May |
2025 |
Our work on generative AI-based single-cell representation learning was presented at ACE Drug Discovery Summit. |
| Apr |
2025 |
Our recent work on generative AI-based single-cell representation learning was accepted at American Association of Cancer Research Annual Meeting. |
| Mar |
2025 |
Our work on generative AI-based single-cell representation learning was presented at Nextgen Omics Spatial & Data. |
| May |
2024 |
I joined Takeda Pharmaceuticals as a research scientist fellow to work on machine learning for cancer biology! |
| May |
2024 |
Honored to receive Takeda Fellowship from Takeda Pharmaceuticals. |
| Apr |
2024 |
Our work on reinforcement learning for robotic disassembly task control was accepted at Journal of Computers & Industrial Engineering. |
| Apr |
2024 |
I gave an invited talk at REMADE Circular Economy Technology Summit & Conference on our recent work on reinforcement learning for robotic disassembly control. |
| Nov |
2023 |
I presented a poster on policy learning for robotic disassembly task control at Northeastern PhD Research Showcase. |
| Nov |
2023 |
Honored to receive Northeastern College of Engineering PhD Research Expo Award. |
| Nov |
2023 |
I presented a poster at Northeastern College of Engineering PhD Research Expo. |
| Apr |
2022 |
Excited to International Symposium on Sustainable Systems and Technology (ISSST) Scholar Award. |
| June |
2023 |
I gave an invited talk at International Symposium on Sustainable Systems and Technology on our recent work on reinforcement learning for disassembly control. |
| Apr |
2022 |
Our recent work on trends in Industry 4.0 was accepted at MDPI Sustainability. |
| May |
2022 |
I passed my candidacy exams and offically became a PhD candidate. |
| Apr |
2022 |
Excited to receive Ferretti & Yamamura Award for Research Excellence for my masters thesis from Northeastern University. |
| Sep |
2021 |
I defended my masters thesis on Reshoring with Remote Manufacturing. |
| Apr |
2022 |
Excited to receive Dell Technologies USA Futuristic Data Science Shout Out Award from Dell Technologies. |
| June |
2020 |
I am interning at Dell Technologies. |
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Prototype Guided Post-pre-training for Alignment in Single Cell Foundational Models
Sachini Weerasekara,
Natasha Darras,
Sagar Kamarthi,
Colles Price,
Jacqueline Isaacs
In review in International Conference on Learning Representations 2027
paper |
code
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REFINEPPO: Learning Continuous Control Policies by Iterative Action Refinement
Sachini Weerasekara,
Sagar Kamarthi,
Jacqueline Isaacs
In review in IEEE International Conference on Robotics and Automation (ICRA) 2027
paper |
code
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Conditional Biases in Large Language Models: How Biased User Turns Modulate In-Context Reasoning
Sachini Weerasekara,
Sagar Kamarthi,
Jacqueline Isaacs
In review in The Nations of the Americas Chapter of the Association for Computational Linguistics (NAACL) 2027
paper |
code
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Reinforcement Learning for Robotic Disassembly Task Control
Sachini Weerasekara,
Wei Li,
Jacqueline Isaacs,
Sagar Kamarthi
CAIE 2024Journal of Computers & Industrial Engineering
paper |
code
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CellClique: Dissecting Tumor Microenvironments at the Single Cell Level Using Generative AI and Spatial Transcriptomics
Sachini Weerasekara,
Natasha Darras,
Nicolas Fernandez,
Melinda Chen,
Alina Ainbinder
Colles Price,
Jacqueline Isaacs
Cancer Research 2025American Association for Cancer Research Annual Meeting
paper
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Improvements to Robotic Disassembly Lot Sizing with Task Planning through Reinforcement Learning
Sachini Weerasekara,
Wei Li,
Jacqueline Isaacs,
Sagar Kamarthi
JAMP 2025
Journal of Advanced Manufacturing and Processing
paper |
code
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Prediction of Clinical Complication Onset Using Neural Point Processes
Sachini Weerasekara,
Jacqueline Isaacs,
Sagar Kamarthi
arXiv
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Trends in Adopting Industry 4.0 for Asset Life Cycle Management for Sustainability: A Keyword Co-occurrence Network Review and Analysis.
Sachini Weerasekara,
Zhenyuan Lu,
Burcu Ozek,
Jacqueline Isaacs,
Sagar Kamarthi
Sustainability 2022Sustainability Journal
paper
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Optimization Methodology for Departure Slots at Slot Coordinated Passenger Airports Based on Processing Element Bottlenecks.
Sachini Weerasekara,
Varuna Adikariwattage,
Nalaka Abeyratne
WTCR 2019World Conference on Transportation Research
paper
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Dissecting tumor microenvironments at the single cell level using generative AI and spatial transcriptomics,
American Association for Cancer Research Annual Meeting, 2025, Chicago, IL.
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Modeling Cell-Neighborhood Interactions using generative AI and spatial transcriptomics,
Nextgen Omics Spatial & Data, 2025, Boston, MA.
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Beyond the Average Cell: Rethinking How Foundation Models Learn Tissue Heterogeneity,
ACE Drug Discovery Summit, 2025, Boston, MA.
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Reinforcement learning for disassembly task control,
REMADE Institute 2024 Circular Economy Technology Summit & Conference, 2024, Washington DC.
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An interpretable deep learning pipeline for predicting pneumonia onset in cardiovascular ICU patients,
Northeastern PhD Research Showcase, 2023, Boston, MA.
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Reinforcement learning agents for decision making in disassembly factory floor,
International Symposium on Sustainable Systems and Technology (ISSST), 2023, Fort Collins, CO.
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Learning for disassembly task control,
Northeastern COE PhD Research Expo, 2023, Boston, MA.
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Takeda Fellow 2024, Fellowship Award from Takeda Pharmaceuticals.
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Northeastern College of Engineering PhD Research Expo Award 2023, Northeastern College of Engineering.
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International Symposium on Sustainable Systems and Technology (ISSST) Scholar Award 2023.
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Ferretti & Yamamura Award for Research Excellence 2022, Northeastern University.
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Dell Technologies USA Futuristic Data Science Shout Out Award, 2022. Dell Technologies.
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IE7300 Machine Learning For Engineering: Teaching Assistant, Northeastern University, 2022 Fall, 2023 Spring, 2023 Summer.
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IE7275 Data Mining in Engineering: Teaching Assistant, Northeastern University, 2021 Spring, 2022 Spring.
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